News Imagerie cellulaire - Cellular imaging
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Portail Emploi CNRS - Offre d'emploi - Chef-fe de projet en Ingénierie logicielle (H/F)

Interlocuteur des équipes de biologistes utilisatrices de l'Infrastructure de Recherche (IR) « France BioImaging » sur des projets nécessitant traitement et analyse d'images, le/la Chef(fe) de projet rejoindra le nouveau service "open DATA" proposé par l'UMS 3714 avec des activités mutualisées et partagées pour les membres des Noeuds Paris-Centre et IPDM de l'IR.
Il/elle aura pour mission d'utiliser, développer et mettre à disposition des outils d'analyse d'images en utilisant les différentes plateformes logicielles disponibles.
Il/elle assurera une veille technologique poussée.

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Non-obstructive intracellular nanolasers

Non-obstructive intracellular nanolasers | News Imagerie cellulaire - Cellular imaging | Scoop.it

Alasdair H. Fikouras, Marcel Schubert, Markus Karl, Jothi D. Kumar, Simon J. Powis, Andrea Di Falco & Malte C. Gather

 

Molecular dyes, plasmonic nanoparticles and colloidal quantum dots are widely used in biomedical optics. Their operation is usually governed by spontaneous processes, which results in broad spectral features and limited signal-to-noise ratio, thus restricting opportunities for spectral multiplexing and sensing. Lasers provide the ultimate spectral definition and background suppression, and their integration with cells has recently been demonstrated. However, laser size and threshold remain problematic. Here, we report on the design, high-throughput fabrication and intracellular integration of semiconductor nanodisk lasers. By exploiting the large optical gain and high refractive index of GaInP/AlGaInP quantum wells, we obtain lasers with volumes 1000-fold smaller than the eukaryotic nucleus (Vlaser < 0.1 µm3), lasing thresholds 500-fold below the pulse energies typically used in two-photon microscopy (Eth ≈ 0.13 pJ), and excellent spectral stability (<50 pm wavelength shift). Multiplexed labeling with these lasers allows cell-tracking through micro-pores, thus providing a powerful tool to study cell migration and cancer invasion.

 

Nature Communications volume 9, Article number: 4817 (2018)

https://doi.org/10.1038/s41467-018-07248-0

Open Access : https://www.nature.com/articles/s41467-018-07248-0.pdf

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Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy

Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy | News Imagerie cellulaire - Cellular imaging | Scoop.it

Youhua Chen, Wenjie Liu, Zhimin Zhang, Cheng Zheng, Yujia Huang, Ruizhi Cao, Dazhao Zhu, Liang Xu, Meng Zhang, Yu-Hui Zhang, Jiannan Fan, Luhong Jin, Yingke Xu, Cuifang Kuang & Xu Liu

 

Imaging and tracking of near-surface three-dimensional volumetric nanoscale dynamic processes of live cells remains a challenging problem. In this paper, we propose a multi-color live-cell near-surface-volume super-resolution microscopy method that combines total internal reflection fluorescence structured illumination microscopy with multi-angle evanescent light illumination. We demonstrate that our approach of multi-angle interference microscopy is perfectly adapted to studying subcellular dynamics of mitochondria and microtubule architectures during cell migration.

 

Nature Communications volume 9, Article number: 4818 (2018)

https://doi.org/10.1038/s41467-018-07244-4

Open Access : https://www.nature.com/articles/s41467-018-07244-4.pdf

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easySLM‐STED: Stimulated emission depletion microscopy with aberration correction, extended field of view and multiple beam scanning

easySLM‐STED: Stimulated emission depletion microscopy with aberration correction, extended field of view and multiple beam scanning | News Imagerie cellulaire - Cellular imaging | Scoop.it
Frederik Görlitz, Stina Guldbrand, Timothy H. Runcorn, Robert T. Murray, Angel L. Jaso‐Tamame, Hugo G. Sinclair, Enrique Martinez‐Perez, James R. Taylor, Mark A. A. Neil, Christopher Dunsby, Paul M. W. French

 

We demonstrate a simplified set‐up for STED microscopy with a straightforward alignment procedure that uses a single spatial light modulator (SLM) with collinear incident excitation and depletion beams to provide phase modulation of the beam profiles and correction of optical aberrations. We show that this approach can be used to extend the field of view for STED microscopy by correcting chromatic aberration that otherwise leads to walk‐off between the focused excitation and depletion beams. We further show how this arrangement can be adapted to increase the imaging speed through multibeam excitation and depletion. Fine adjustments to the alignment can be accomplished using the SLM only, conferring the potential for automation.

 

J. Biophotonics Vol.11, Issue11, Nov. 2018, e201800087

https://doi.org/10.1002/jbio.201800087

Open Access : https://onlinelibrary.wiley.com/doi/epdf/10.1002/jbio.201800087

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In vivo study of rat cortical hemodynamics using a stereotaxic‐apparatus‐compatible photoacoustic microscope

In vivo study of rat cortical hemodynamics using a stereotaxic‐apparatus‐compatible photoacoustic microscope | News Imagerie cellulaire - Cellular imaging | Scoop.it
Heng Guo, Qian Chen, Weizhi Qi, Xingxing Chen, Lei Xi

 

Brain imaging is an important technique in cognitive neuroscience. In this article, we designed a stereotaxic‐apparatus‐compatible photoacoustic microscope for the studies of rat cortical hemodynamics. Compared with existing optical resolution photoacoustic microscopy (ORPAM) systems, the probe owns feature of fast, light and miniature. In this microscope, we integrated a miniaturized ultrasound transducer with a center frequency of 10 MHz to detect photoacoustic signals and a 2‐dimensional (2D) microelectromechanical system (MEMS) scanner to achieve raster scanning of the optical focus. Based on phantom evaluation, this imaging probe has a high lateral resolution of 3.8 μm and an effective imaging domain of 2 × 2 mm2. Different from conventional ORPAMs, combining with standard stereotaxic apparatus enables broad studies of rodent brains without any motion artifact. To show its capability, we successfully captured red blood cell flow in the capillary, monitored the vascular changes during bleeding and blood infusion and visualized cortical hemodynamics induced by middle cerebral artery occlusion.

 

J. Biophotonics Vol.11, Issue9, Sept. 2018, e201800067

https://doi.org/10.1002/jbio.201800067

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Dual‐wavelength hybrid optoacoustic‐ultrasound biomicroscopy for functional imaging of large‐scale cerebral vascular networks

Dual‐wavelength hybrid optoacoustic‐ultrasound biomicroscopy for functional imaging of large‐scale cerebral vascular networks | News Imagerie cellulaire - Cellular imaging | Scoop.it
Johannes Rebling, Héctor Estrada, Sven Gottschalk, Gali Sela, Michael Zwack, Georg Wissmeyer, Vasilis Ntziachristos, Daniel Razansky

 

A critical link exists between pathological changes of cerebral vasculature and diseases affecting brain function. Microscopic techniques have played an indispensable role in the study of neurovascular anatomy and functions. Yet, investigations are often hindered by suboptimal trade‐offs between the spatiotemporal resolution, field‐of‐view (FOV) and type of contrast offered by the existing optical microscopy techniques. We present a hybrid dual‐wavelength optoacoustic (OA) biomicroscope capable of rapid transcranial visualization of large‐scale cerebral vascular networks. The system offers 3‐dimensional views of the morphology and oxygenation status of the cerebral vasculature with single capillary resolution and a FOV exceeding 6 × 8 mm2, thus covering the entire cortical vasculature in mice. The large‐scale OA imaging capacity is complemented by simultaneously acquired pulse‐echo ultrasound (US) biomicroscopy scans of the mouse skull. The new approach holds great potential to provide better insights into cerebrovascular function and facilitate efficient studies into neurological and vascular abnormalities of the brain.

 

J. Biophotonics Vol.11, Issue9, Sept. 2018, e201800057

https://doi.org/10.1002/jbio.201800057

Open Access : https://onlinelibrary.wiley.com/doi/epdf/10.1002/jbio.201800057

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Pulsed interleaved excitation-based line-scanning spatial correlation spectroscopy (PIE-lsSCS)

Pulsed interleaved excitation-based line-scanning spatial correlation spectroscopy (PIE-lsSCS) | News Imagerie cellulaire - Cellular imaging | Scoop.it

Xiang Gao, Peng Gao, Benedikt Prunsche, Karin Nienhaus & Gerd

Ulrich Nienhaus

 

We report pulsed interleaved excitation (PIE) based line-scanning spatial correlation spectroscopy (PIE-lsSCS), a quantitative fluorescence microscopy method for the study of dynamics in free-standing lipid bilayer membranes. Using a confocal microscope, we scan multiple lines perpendicularly through the membrane, each one laterally displaced from the previous one by several ten nanometers. Scanning through the membrane enables us to eliminate intensity fluctuations due to membrane displacements with respect to the observation volume. The diffusion of fluorescent molecules within the membrane is quantified by spatial correlation analysis, based on the fixed lag times between successive line scans. PIE affords dual-color excitation within a single line scan and avoids channel crosstalk. PIE-lsSCS data are acquired from a larger membrane region so that sampling is more efficient. Moreover, the local photon flux is reduced compared with single-point experiments, resulting in a smaller fraction of photobleached molecules for identical exposure times. This is helpful for precise measurements on live cells and tissues. We have evaluated the method with experiments on fluorescently labeled giant unilamellar vesicles (GUVs) and membrane-stained live cells.

 

Scientific Reports volume 8, Article number: 16722 (2018)

https://doi.org/10.1038/s41598-018-35146-4

Open Access : https://www.nature.com/articles/s41598-018-35146-4.pdf

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Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics | News Imagerie cellulaire - Cellular imaging | Scoop.it

Andrea Attardi, Timothy Fulton, Maria Florescu, Gopi Shah, Leila Muresan, Martin O. Lenz, Courtney Lancaster, Jan Huisken, Alexander van Oudenaarden and Benjamin Steventon

 

During gastrulation, embryonic cells become specified into distinct germ layers. In mouse, this continues throughout somitogenesis from a population of bipotent stem cells called neuromesodermal progenitors (NMps). However, the degree of self-renewal associated with NMps in the fast-developing zebrafish embryo is unclear. Using a genetic clone-tracing method, we labelled early embryonic progenitors and found a strong clonal similarity between spinal cord and mesoderm tissues. We followed individual cell lineages using light-sheet imaging, revealing a common neuromesodermal lineage contribution to a subset of spinal cord tissue across the anterior-posterior body axis. An initial population subdivides at mid-gastrula stages and is directly allocated to neural and mesodermal compartments during gastrulation. A second population in the tailbud undergoes delayed allocation to contribute to the neural and mesodermal compartment only at late somitogenesis. Cell tracking and retrospective cell fate assignment at late somitogenesis stages reveal these cells to be a collection of mono-fated progenitors. Our results suggest that NMps are a conserved population of bipotential progenitors, the lineage of which varies in a species-specific manner due to vastly different rates of differentiation and growth.

 

Development 2018 145: dev166728

doi: 10.1242/dev.166728

Open Access : http://dev.biologists.org/content/145/21/dev166728.full-text.pdf?with-ds=yes

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Deep learning to predict microscope images

Deep learning to predict microscope images | News Imagerie cellulaire - Cellular imaging | Scoop.it

Roger Brent and Laura Boucheron

 

A type of neural network first described in 2015 can be trained to translate between images of the same field of view acquired by different modalities. Trained networks can use information inherent in grayscale images of cells to predict fluorescent signals.

 

Nature Methods volume 15, pages868–870 (2018)

https://doi.org/10.1038/s41592-018-0194-9

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Fast, in vivo voltage imaging using a red fluorescent indicator

Fast, in vivo voltage imaging using a red fluorescent indicator | News Imagerie cellulaire - Cellular imaging | Scoop.it

Madhuvanthi Kannan, Ganesh Vasan, Cheng Huang, Simon Haziza, Jin Zhong Li, Hakan Inan, Mark J. Schnitzer and Vincent A. Pieribone

 

Genetically encoded voltage indicators (GEVIs) are emerging optical tools for acquiring brain-wide cell-type-specific functional data at unparalleled temporal resolution. To broaden the application of GEVIs in high-speed multispectral imaging, we used a high-throughput strategy to develop voltage-activated red neuronal activity monitor (VARNAM), a fusion of the fast Acetabularia opsin and the bright red fluorophore mRuby3. Imageable under the modest illumination intensities required by bright green probes (<50 mW mm−2), VARNAM is readily usable in vivo. VARNAM can be combined with blue-shifted optical tools to enable cell-type-specific all-optical electrophysiology and dual-color spike imaging in acute brain slices and live Drosophila. With enhanced sensitivity to subthreshold voltages, VARNAM resolves postsynaptic potentials in slices and cortical and hippocampal rhythms in freely behaving mice. Together, VARNAM lends a new hue to the optical toolbox, opening the door to high-speed in vivo multispectral functional imaging.

 

Nature Methods (2018) Published: 12 November 2018

https://doi.org/10.1038/s41592-018-0188-7

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Perspective: Wavefront shaping techniques for controlling multiple light scattering in biological tissues: Toward in vivo applications

Perspective: Wavefront shaping techniques for controlling multiple light scattering in biological tissues: Toward in vivo applications | News Imagerie cellulaire - Cellular imaging | Scoop.it

Jung-Hoon Park, Zhipeng Yu, KyeoReh Lee, Puxiang Lai and YongKeun Park

 

Multiple light scattering has been regarded as a barrier in imaging through complex media such as biological tissues. Owing to recent advances in wavefront shaping techniques, optical imaging through intact biological tissues without invasive procedures can now be used for direct experimental studies, presenting promising application opportunities in in vivo imaging and diagnosis. Although most of the recent proof of principle breakthroughs have been achieved in the laboratory setting with specialties in physics and engineering, we anticipate that these technologies can be translated to biological laboratories and clinical settings, which will revolutionize how we diagnose and treat a disease. To provide insight into the physical principle that enables the control of multiple light scattering in biological tissues and how recently developed techniques can improve bioimaging through thick tissues, we summarize recent progress on wavefront shaping techniques for controlling multiple light scattering in biological tissues.

 

APL Photonics 3, 100901 (2018)

https://doi.org/10.1063/1.5033917

Open Access : https://aip.scitation.org/doi/pdf/10.1063/1.5033917

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Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells

Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells | News Imagerie cellulaire - Cellular imaging | Scoop.it

Malinda S. Thilakarathna and Manish N. Raizada

 

Microbial symbiotic nitrogen fixation (SNF) occurs inside root nodules, where fixed-N (NH4+) from rhizobia is first assimilated into the amino acid glutamine (Gln). Visualization of Gln dynamics in nodulated root systems of different plant species would require re-engineering transgenic Gln reporters specific for each rhizobia/host genotype. Here we demonstrate the use of companion biosensor cells called GlnLux (Escherichia coli auxotrophic for Gln and constitutively expressing lux) to image Gln accumulation in nodulated root systems across a diversity of legume/rhizobia species. Companion GlnLux cells are embedded into agar (GlnLux agar) upon which legume root systems are placed following freeze-thawing to cause Gln leakage. Photons released from nearby activated biosensor cells are captured using a photon capture camera. Using split root systems, we demonstrate that in diverse amide-exporting legumes (alfalfa, lentil, and green pea) and a ureide-exporting legume (soybean) that GlnLux agar imaging is sufficiently sensitive to detect Gln release from individual nodules and can differentiate root systems with active nif+ from inactive nif− nodules. The assay permits visualization of both source and sink dynamics of nodule Gln, specifically, Gln import into nodules from roots (for nodule growth and/or amino acid cycling), Gln assimilated from fixed nitrogen that accumulates inside nodules, and Gln export from nodules into roots from this assimilatory-N. GlnLux agar-based imaging is thus a new research tool to localize the accumulation and transfer of a critical amino acid required for rhizobia symbionts within legume phytobiomes. We discuss the ability of this technology to open new frontiers in basic research and its limitations.

Phytobiomes Journal 2018, Volume 2, Number 3 Pages 117-128


Via Jean-Michel Ané
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Near-infrared STED nanoscopy with an engineered bacterial phytochrome

Near-infrared STED nanoscopy with an engineered bacterial phytochrome | News Imagerie cellulaire - Cellular imaging | Scoop.it

Maria Kamper, Haisen Ta, Nickels A. Jensen, Stefan W. Hell, Stefan Jakobs

 

The near infrared (NIR) optical window between the cutoff for hemoglobin absorption at 650 nm and the onset of increased water absorption at 900 nm is an attractive, yet largely unexplored, spectral regime for diffraction-unlimited super-resolution fluorescence microscopy (nanoscopy). We developed the NIR fluorescent protein SNIFP, a bright and photostable bacteriophytochrome, and demonstrate its use as a fusion tag in live-cell microscopy and STED nanoscopy. We further demonstrate dual color red-confocal/NIR-STED imaging by co-expressing SNIFP with a conventional red fluorescent protein.

 

Nature Communications volume 9, Article number: 4762 (2018)

https://doi.org/10.1038/s41467-018-07246-2

Open Access : https://www.nature.com/articles/s41467-018-07246-2.pdf

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In vivo multiphoton microscopy detects longitudinal metabolic changes associated with delayed skin wound healing

In vivo multiphoton microscopy detects longitudinal metabolic changes associated with delayed skin wound healing | News Imagerie cellulaire - Cellular imaging | Scoop.it

Jake D. Jones, Hallie E. Ramser, Alan E. Woessner & Kyle P. Quinn

 

Chronic wounds are difficult to diagnose and characterize due to a lack of quantitative biomarkers. Label-free multiphoton microscopy has emerged as a useful imaging modality capable of quantifying changes in cellular metabolism using an optical redox ratio of FAD/(NADH+FAD) autofluorescence. However, the utility of an optical redox ratio for long-term in vivo monitoring of tissue metabolism has not been robustly evaluated. In this study, we demonstrate how multiphoton microscopy can be used to monitor changes in the metabolism of individual full-thickness skin wounds in vivo. 3D optical redox ratio maps and NADH fluorescence lifetime images identify differences between diabetic and control mice during the re-epithelialization of wounds. These metabolic changes are associated with a transient increase in keratinocyte proliferation at the wound edge. Our study demonstrates that high-resolution, non-invasive autofluorescence imaging can be performed in vivo and that optical redox ratios can serve as quantitative optical biomarkers of impaired wound healing.

 

Communications Biology volume 1, Article number: 198 (2018)

https://doi.org/10.1038/s42003-018-0206-4

Open Access : https://www.nature.com/articles/s42003-018-0206-4.pdf

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Modular approach for resolving and mapping complex neural and other cellular structures and their associated deformation fields in three dimensions

Modular approach for resolving and mapping complex neural and other cellular structures and their associated deformation fields in three dimensions | News Imagerie cellulaire - Cellular imaging | Scoop.it

Mark T. Scimone, Harry C. Cramer III, Eyal Bar-Kochba, Rodolfo Amezcua, Jonathan B. Estrada & Christian Franck

 

Understanding the biological implications of cellular mechanotransduction, especially in the context of pathogenesis, requires the accurate resolution of material deformation and strain fields surrounding the cells. This is particularly challenging for cells displaying branched, 3D architectures. Here, we provide a modular approach for 3D image segmentation and strain mapping of topologically complex structures. We describe how to use our approach, using neural cells and networks as an example. In addition to describing how to implement the computational analysis, we provide details of a cell culture protocol that can be used to generate neural networks for analysis and experimentation. This protocol allows for transformation of matrix-induced strains, and their full resolution across single cells or networks in three dimensions. The protocol also provides analyses to compute both the locally varying cytoskeletal strains and the average strain experienced by cells. An additional module allows spatial correlation of these strain maps with cytoskeletal features, including neurite disruptions such as neuronal blebs. Image processing and strain mapping take ≥3 h, with the exact time required being dependent on use case, software familiarity, and file size.

 

Nature Protocols (2018) Published: 19 November 2018

https://doi.org/10.1038/s41596-018-0077-7

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Enhanced mRNA FISH with compact quantum dots

Enhanced mRNA FISH with compact quantum dots | News Imagerie cellulaire - Cellular imaging | Scoop.it

Yang Liu, Phuong Le, Sung Jun Lim, Liang Ma, Suresh Sarkar, Zhiyuan Han, Stephen J. Murphy, Farhad Kosari, George Vasmatzis, John C. Cheville & Andrew M. Smith

 

Fluorescence in situ hybridization (FISH) is the primary technology used to image and count mRNA in single cells, but applications of the technique are limited by photophysical shortcomings of organic dyes. Inorganic quantum dots (QDs) can overcome these problems but years of development have not yielded viable QD-FISH probes. Here we report that macromolecular size thresholds limit mRNA labeling in cells, and that a new generation of compact QDs produces accurate mRNA counts. Compared with dyes, compact QD probes provide exceptional photostability and more robust transcript quantification due to enhanced brightness. New spectrally engineered QDs also allow quantification of multiple distinct mRNA transcripts at the single-molecule level in individual cells. We expect that QD-FISH will particularly benefit high-resolution gene expression studies in three dimensional biological specimens for which quantification and multiplexing are major challenges.

 

Nature Communications volume 9, Article number: 4461 (2018)

https://doi.org/10.1038/s41467-018-06740-x

Open Access : https://www.nature.com/articles/s41467-018-06740-x.pdf

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Quantitative assessment of cell contractility using polarized light microscopy

Quantitative assessment of cell contractility using polarized light microscopy | News Imagerie cellulaire - Cellular imaging | Scoop.it
Wenjun Wang, Joseph P. Miller, Susan C. Pannullo, Cynthia A. Reinhart‐King, Francois Bordeleau

 

Cell contractility regulates multiple cell behaviors which contribute to both normal and pathological processes. However, measuring cell contractility remains a technical challenge in complex biological samples. The current state of the art technologies employed to measure cell contractility have inherent limitations that greatly limit the experimental conditions under which they can be used. Here, we use quantitative polarization microscopy to extract information about cell contractility. We show that the optical retardance signal measured from the cell body is proportional to cell contractility in 2‐dimensional and 3‐dimensional platforms, and as such can be used as a straightforward, tractable methodology to assess cell contractility in a variety of systems. This label‐free optical method provides a novel and flexible way to assess cellular forces of single cells and monolayers in several cell types, fixed or live, in addition to cells present in situ in mouse tumor tissue samples. This easily implementable and experimentally versatile method will significantly contribute to the cell mechanics field.

 

J. Biophotonics Vol.11, Issue11, Nov. 2018, e201800008

https://doi.org/10.1002/jbio.201800008

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High‐throughput light sheet tomography platform for automated fast imaging of whole mouse brain

High‐throughput light sheet tomography platform for automated fast imaging of whole mouse brain | News Imagerie cellulaire - Cellular imaging | Scoop.it
Xiong Yang, Qi Zhang, Fei Huang, Ke Bai, Yiming Guo, Yongsheng Zhang, Ning Li, Yuting Cui, Pei Sun, Shaoqun Zeng, Xiaohua Lv

 

Acquiring information of the neural structures in the whole‐brain level is vital for systematically exploring mechanisms and principles of brain function and dysfunction. Most methods for whole brain imaging, while capable of capturing the complete morphology of neurons, usually involve complex sample preparation and several days of image acquisition. The whole process including optical clearing or resin embedding is time consuming for a quick survey of the distribution of specific neural circuits in the whole brain. Here, we develop a high‐throughput light‐sheet tomography platform (HLTP), which requires minimum sample preparation. This method does not require optical clearing for block face light sheet imaging. After fixation using paraformaldehyde, an aligned 3 dimensional image dataset of a whole mouse brain can be obtained within 5 hours at a voxel size of 1.30 × 1.30 × 0.92 μm. HLTP could be a very efficient tool for quick exploration and visualization of brain‐wide distribution of specific neurons or neural circuits.

 

J. Biophotonics Vol.11, Issue9, Sept. 2018, e201800047

https://doi.org/10.1002/jbio.201800047

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Correlative Light-Electron Microscopy detects lipopolysaccharide and its association with fibrin fibres in Parkinson’s Disease, Alzheimer’s Disease and Type 2 Diabetes Mellitus

Correlative Light-Electron Microscopy detects lipopolysaccharide and its association with fibrin fibres in Parkinson’s Disease, Alzheimer’s Disease and Type 2 Diabetes Mellitus | News Imagerie cellulaire - Cellular imaging | Scoop.it

Greta M. de Waal, Lize Engelbrecht, Tanja Davis, Willem J. S. de

Villiers, Douglas B. Kell & Etheresia Pretorius

 

Many chronic diseases, including those classified as cardiovascular, neurodegenerative, or autoimmune, are characterized by persistent inflammation. The origin of this inflammation is mostly unclear, but it is typically mediated by inflammatory biomarkers, such as cytokines, and affected by both environmental and genetic factors. Recently circulating bacterial inflammagens such as lipopolysaccharide (LPS) have been implicated. We used a highly selective mouse monoclonal antibody to detect bacterial LPS in whole blood and/or platelet poor plasma of individuals with Parkinson’s Disease, Alzheimer’s type dementia, or Type 2 Diabetes Mellitus. Our results showed that staining is significantly enhanced (P < 0.0001) compared to healthy controls. Aberrant blood clots in these patient groups are characterized by amyloid formation as shown by the amyloid-selective stains thioflavin T and Amytracker™ 480 or 680. Correlative Light-Electron Microscopy (CLEM) illustrated that the LPS antibody staining is located in the same places as where amyloid fibrils may be observed. These data are consistent with the Iron Dysregulation and Dormant Microbes (IDDM) hypothesis in which bacterial inflammagens such as LPS are responsible for anomalous blood clotting as part of the aetiology of these chronic inflammatory diseases.

 

Scientific Reports volume 8, Article number: 16798 (2018)

https://doi.org/10.1038/s41598-018-35009-y

Open Access : https://www.nature.com/articles/s41598-018-35009-y.pdf

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Looking deep inside the phloem and xylem cell wall composition

Looking deep inside the phloem and xylem cell wall composition | News Imagerie cellulaire - Cellular imaging | Scoop.it

Plant cells are surrounded by a rigid frame, called cell wall. These walls are highly complex structures whose composition and organization changes along plant growth and development. On the other hand, the development of the phloem and xylem vascular cells, which participate in the transport of sugars and water as well as support, can be influenced by cell-specific cell wall composition. Rozenn Le Hir and colleagues from the CATS team (Carbon Allocation, Transport and Signaling) from the Institut Jean-Pierre Bourgin (INRA/AgroParisTech/CNRS/UPSaclay, Versailles) used the power provided by the synchrotron SOLEIL at the SMIS beamline to analyze in details the cell wall composition of a wild-type and a double mutant sweet11-1sweet12-1, which impairs sugar transport, in the Arabidopsis floral stem vascular tissue. They used a combination of synchrotron radiation-based FTIR, Raman spectroscopy and multivariate analysis to show that in addition to modified overall xylem cell wall composition, phloem cell walls in the double mutant line were characterized by modified hemicellulose composition. Additionally, the disruption of SWEET11 and SWEET12 genes impacts xylem cell wall composition in a cell-specific manner, with changes in hemicelluloses and cellulose observed at the xylem vessel interface. These results, published in J Experimental Botany suggest that the facilitated transport of sugars between vascular parenchyma cells and conducting cells is important to ensuring correct phloem and xylem cell wall composition.

 

Contact : rozenn.le-hir@inra.fr


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An inner light

An inner light | News Imagerie cellulaire - Cellular imaging | Scoop.it

Michael Eisenstein

 

In vivo bioluminescence imaging offers a non-invasive look inside the body. Its future looks bright.

 

Lab Animal volume 47, pages301–304 (2018)

https://doi.org/10.1038/s41684-018-0174-9

Open Access : https://www.nature.com/articles/s41684-018-0174-9.pdf

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Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy | News Imagerie cellulaire - Cellular imaging | Scoop.it

Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman and Gregory R. Johnson

 

Understanding cells as integrated systems is central to modern biology. Although fluorescence microscopy can resolve subcellular structure in living cells, it is expensive, is slow, and can damage cells. We present a label-free method for predicting three-dimensional fluorescence directly from transmitted-light images and demonstrate that it can be used to generate multi-structure, integrated images. The method can also predict immunofluorescence (IF) from electron micrograph (EM) inputs, extending the potential applications.

 

Nature Methods volume 15pages917–920 (2018)

https://doi.org/10.1038/s41592-018-0111-2

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Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope

Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope | News Imagerie cellulaire - Cellular imaging | Scoop.it

Dalton R. Gibbs , Anisa Kaur, Anoja Megalathan, Kumar Sapkota and Soma Dhakal

 

Prism-based total internal reflection fluorescence (pTIRF) microscopy is one of the most widely used techniques for the single molecule analysis of a vast range of samples including biomolecules, nanostructures, and cells, to name a few. It allows for excitation of surface bound molecules/particles/quantum dots via evanescent field of a confined region of space, which is beneficial not only for single molecule detection but also for analysis of single molecule dynamics and for acquiring kinetics data. However, there is neither a commercial microscope available for purchase nor a detailed guide dedicated for building this microscope. Thus far, pTIRF microscopes are custom-built with the use of a commercially available inverted microscope, which requires high level of expertise in selecting and handling sophisticated instrument-parts. To directly address this technology gap, here we describe a step-by-step guide on how to build and characterize a pTIRF microscope for in vitro single-molecule imaging, nanostructure analysis and other life sciences research.

 

Methods Protoc. 2018, 1(4), 40
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Invited Article: Saturation scattering competition for non-fluorescence single-wavelength super-resolution imaging

Invited Article: Saturation scattering competition for non-fluorescence single-wavelength super-resolution imaging | News Imagerie cellulaire - Cellular imaging | Scoop.it

Xueying Ouyang, Fei Qin, Ziheng Ji, Tianyue Zhang, Jian Xu, Ziwei Feng, Shenyu Yang, Yaoyu Cao, Kebin Shi, Lingxiang Jiang and Xiangping Li

 

Stimulated emission depletion nanoscopy and its derivatives based on saturation induced competition effects have become an indispensable tool for studying cellular events and their dynamics in living conditions. The successful implementation of these techniques heavily relies on the competition between excitation induced spontaneous emission and stimulated emission from fluorescent dyes. The use of two laser beams at different wavelengths perplexes the optical system and the high intensity saturation beam inevitably introduces detrimental photobleaching effects. Harnessing the emerging saturation scattering of plasmonic nanoparticles, here, we demonstrate a novel fluorescence-free single-wavelength super-resolution imaging technique using gold nanoparticles. A lateral resolution of 101.2 nm (<λ/5) is achieved through introducing saturation scattering competition (SSC) of 60 nm gold nanospheres between dual beams at the same wavelength. In addition, the SSC drastically reduces the saturation intensity by three orders of magnitude than the conventional stimulated emission depletion process at comparable resolutions. As a proof of concept, we realized robust single-wavelength super-resolved imaging in dMG-63 cells with a simplified system. The current technique provides a new modality of biosample-friendly technology for optical super-resolution imaging.

 

APL Photonics 3, 110801 (2018)

https://doi.org/10.1063/1.5043533

Open Access : https://aip.scitation.org/doi/pdf/10.1063/1.5043533

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Deciphering the immune microenvironment of a tissue by digital imaging and cognition network

Deciphering the immune microenvironment of a tissue by digital imaging and cognition network | News Imagerie cellulaire - Cellular imaging | Scoop.it

A. Lopès, Al H. Cassé, E. Billard, E. Boulcourt-Sambou, G. Roche, C.

Larois, N. Barnich, S. Naimi, M. Bonnet & B. Dumas

 

Evidence has highlighted the importance of immune cells in various gut disorders. Both the quantification and localization of these cells are essential to the understanding of the complex mechanisms implicated in these pathologies. Even if quantification can be assessed (e.g., by flow cytometry), simultaneous cell localization and quantification of whole tissues remains technically challenging. Here, we describe the use of a computer learning-based algorithm created in the Tissue Studio interface that allows for a semi-automated, robust and rapid quantitative analysis of immunofluorescence staining on whole colon sections according to their distribution in different tissue areas. Indeed, this algorithm was validated to characterize gut immune microenvironment. Its application to the preclinical colon cancer APCMin/+ mouse model is illustrated by the simultaneous counting of total leucocytes and T cell subpopulations, in the colonic mucosa, lymphoid follicles and tumors. Moreover, we quantify T cells in lymphoid follicles for which quantification is not possible with classical methods. Thus, this algorithm is a new and robust preclinical research tool, for investigating immune contexture exemplified by T cells but it is also applicable to other immune cells such as other myeloid and lymphoid populations or other cellular phenomenon along mouse gut.

 

Scientific Reports volume 8, Article number: 16692 (2018)

https://doi.org/10.1038/s41598-018-34731-x

Open Access : https://www.nature.com/articles/s41598-018-34731-x.pdf

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